MICROBIAL PHYSIOLOGY

By the same authors

Essentials of Virology S. Ram Reddy & S.M. Reddy

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MICROBIAL PHYSIOLOGY

S. Ram Reddy Professor, Department of Microbiology Kakatiya University, Warangal (India)

and S.M. Reddy

Professor Emeritus, Department of Botany, Kakatiya University, Warangal (India)

SCIENTIFIC PUBLISHERS (INDIA) P.O. Box 91 JODHPUR

Published by: Pawan Kumar Scientific Publishers (India) 5-A, New Pali Road, P.O. Box 91 JODHPUR – 342 001 E-mail: info@scientificpub.com Print, 2008 ISBN: 978-81-7233-529-8 (H.B.) 978-81-7233-530-4 (P.B.) eISBN: 978-93-87913-19-6 © Reddy & Reddy, 2005 Laser typeset : Rajesh Ojha Printed in India

Preface

Microbial physiology is a field that is experiencing rapid growth and making inroads to allied disciplines like biochemistry, biophysics, genetics and molecular biology. Physiology and metabolism are twins and it is difficult to decide where physiology leaves off and metabolism begins. Similarly, it is difficult to draw a borderline between physiology and related subjects like nutrition, biochemistry and genetics. The difficulties in understanding the microbial physiology are confound probably due to the fact that micro-organisms display a bewildering physiological and metabolic diversity. Further, a particular organelle like cell membrane carry a multitude of physiological and biochemical functions. Similarly, microbial physiology is not properly understood without substantial consideration of genetic make up and of the basic principles of molecular biology.

The role of microorganisms in nature and in human life activities is a matter that has been reckoned so poignantly than ever before. Microbial physiology is the heart of different disciplines of microbiology. All the activities of microbes are the different manifestations of basic physiological activities. Thus the understandings of the physiology of the microbes enable us in manipulating these organisms in a desired direction.

Though there are several books available dealing with microbial physiology to different depths, a comprehensive book covering all aspects of physiology and catering the needs of students, teachers and researchers is a long felt need. The present book is basically designed to fill this vacuum and it may serve users as a textbook or reference book as it is written in a flexible manner covering the basic aspects and at the same time projecting the expanding areas of the subject.

The layout of the chapters and contents of the chapters are planned in such way to provide the principles of microbial physiology in a right perspective. Chapters I to VI are intended to provide basic information on cell structure, nutrition, growth and bioenergetics and environmental adaptations. Chapters VII to X provide a picture how different

vi Microbial Physiology

microorganisms obtain energy and carbon for synthetic or anabolic processes. Chapters XI – XIII deal with the catabolic processes under diverse conditions. The diversity of both catabolic and anabolic processes of microorganisms are also discussed. The last three chapters explain the biological nitrogen fixation; secondary metabolism and sporulation, which are specific to microorganisms and at the same time, provide basic information necessary to exploit them for biotechnological purposes. We have deliberately omitted some topics like amino acid, protein and nucleic acid metabolism, which are almost similar in all biological systems, and the information can be obtained from any book.

It is hoped that the contents of this book fulfill the needs of students of undergraduate and post-graduate as well as teachers of microbiology of all Indian Universities. An attempt has been made to present the subject in a simple and lucid manner avoiding too much of quantitative information. Suggested readings are provided at the end of each chapter for the benefit of those who intend in depth of the subject. Authors have taken every care to present the facts of the subject matter. However, they are conscious of their limitations and invite suggestions, which will go a along way for improving the subject matter and the book in future.

4th September, 2004 S. Ram Reddy

S.M. Reddy

Acknowledgements

We are grateful to many people who are instrumental in bringing out this book to light. First, we express our indebtedness to our great teachers Late Prof. R.N. Tandon and Late Prof. K.S. Bilgrami who have baptized us to the fascinating and challenging field of microbial physiology. Our teaching for the last three decades to undergraduate and post-graduate students has widened the horizons and increased the depth of the subject. Classroom teaching, seminars and discussions with students have really made us to realize the necessity to bring out a comprehensive book on this subject. Their response to the course material was instrumental in its conversion to a text. The research work of our Ph.D. students who have worked on different aspects of microbial physiology helped us to probe different areas and thus enriched our knowledge and infused a confidence in bringing out this book.

We have consulted a large number of books, original research papers and review articles available on the subject and liberally borrowed the subject matter. We express our indebtedness to the publishers and authors of these sources.

Our family members were always cooperative and have shown keen interest in this project. Without the untiring help of our student, Dr. P. Pavan Kumar, compilation of subject index and glossary would not have been possible. He spent long hours at computer to transform our hand-written manuscript to computer manuscript.

The partial financial assistance in the form of publication grant from University Grants Commission is gratefully acknowledged.

We are also thankful to Shri. Pawan Kumar, M/s Scientific Publishers (India), Jodhpur for bringing out this book timely and in an excellent format and design.

Contents

Preface v Acknowledgements vii

CHAPTER 1 Cell structure and function 1 1.1 Introduction 1 1.2 Prokaryotes vs eukaryotes 1 1.3 Prokaryotic cell structure 3 1.4 Further reading 10

CHAPTER 2

Cell wall and its biosynthesis 11 2.1 Introduction 11 2.2 Types of cell walls 11 2.3 Peptidoglycan 12 2.4 Gram-positive cell wall 15 2.5 Gram-negative cell wall 16 2.6 Archaeal cell wall 17 2.7 Protoplasts and spheroplasts 18 2.8 Synthesis of gram-positive cell wall 19 2.9 Synthesis of gram negative cell wall 22 2.10 Expolysaccharides 25 2.11 Further reading 27

CHAPTER 3

Bioenergetics 29 3.1 Metabolism 29 3.2 Bioenergetics 34

3.3 Laws of thermodynamics 35 3.4 Coupled reactions 38 3.5 Role of ATP 38 3.6 Oxidation - reduction reactions 39 3.7 Transduction of energy 41 3.8 Chemiosmotic theory 45 3.9 ATP synthase 46 3.10 ATP synthesis 47 3.11 Bioenergetics in cytosol 48 3.12 Energy rich compounds 50 3.13 ATP and cell yields 52 3.14 Further reading 53

CHAPTER 4

Nutrition 55 4.1 Introduction 55 4.2 Composition of microbial cell 56 4.3 Classification of nutrients 57 4.4 Culture media 60 4.5 Nutritional classification of

microorganisms 62 4.6 Uptake and transport of nutrients 63 4.7 Transport of iron 69 4.8 Efflux of substances 70 4.9 Further reading 70

CHAPTER 5

Microbial Growth 71 5.1 Introduction 71 5.2 Definition 71

Contents x

5.3 Growth curve 72 5.4 Growth kinetics 74 5.5 Synchronous growth 78 5.6 Diauxic growth 79 5.7 Growth yields 80 5.8 Energetics of growth 80 5.9 The continuous culture 81 5.10 Balanced and unbalanced growth 82 5.11 Measurement of microbial growth 83 5.12 The influence of environmental factors on

growth 87 5.13 Microbial growth in natural

environment 94 5.14 Further reading 95

CHAPTER 6

Homeostasis 96 6.1 Definition 96 6.2 Maintenance of constancy of pH 96 6.3 Maintenance of constancy of osmolarity 97 6.4 The heat shock response 99 6.5 Starvation and survival 100 6.6 Further reading 106

CHAPTER 7

Phototrophy 108

7.1 Phototrophy 108 7.2 Photosynthesis 109 7.3 Diversity of phototrophs 109 7.4 Photosynthetic pigments 113 7.5 Physiology of photosynthesis 117 7.6 Bacteriorhodopsin and light mediated

ATP synthesis 128 7.7 Halorhodopsin, a light-driven chloride

pump 131 7.8 Further reading 131

CHAPTER 8

Chemolithoautotrophy 133

8.1 Definition 133 8.2 Energetics of chemolithotrophy 135 8.3 Nitrifiers 136 8.4 Sulphur oxidizers 140 8.5 Iron bacteria 144 8.6 Hydrogen bacteria 146

8.7 Carboxydobacteria 147 8.8 Further reading 148

CHAPTER 9

Chemoheterotrophy

9.1. Acetogens 149 9.1.1 Introduction 149 9.1.2 Distribution and taxonomy 149 9.1.3 CO2 metabolism and acetogenesis 150 9.1.4 Further reading 155

CHAPTER 9

Chemoheterotrophy

9.2. Methanogens 156 9.2.1. Introduction 156 9.2.2. General characteristics 156 9.2.3. Habitat 157 9.2.4. Diversity and phylogeny 158 9.2.5. Physiology 160 9.2.6. Economic importance 166 9.2.7. Further reading 167

CHAPTER 9

Chemoheterotrophy

9.3. Methylotrophs 168 9.3.1 Introduction 168 9.3.2 Taxonomy and systematic position 168 9.3.3 Physiology 170 9.3.4 Applications of methylotrophs 174 9.3.5 Further reading 175

CHAPTER 9

Chemoheterotrophy

9.4. Hydrocarbon utilizers 176 9.4.1 Introduction 176 9.4.2 Oxygenases 178 9.4.3 Metabolism of aliphatic hydrocarbons 178 9.4.4 Metabolism of aromatic hydrocarbons 179 9.4.5 Hydrocarbon utilizers and

bioremediation 187 9.4.6 Hydrocarbon utilizers and oil

exploration 188 9.4.7 Further reading 188

Contents xi

CHAPTER 10

Assimilation of complex carbohydrates and proteins 190

10.1 Introduction 190 10.2 Cellulose 190 10.3 Hemicellulose 197 10.4 Starch 198 10.5 Pectin 201 10.6 Chitin 204 10.7 Proteins 204 10.8 Further reading 208

CHAPTER 11

Aerobic respiration 209 11.1 Introduction 209 11.2 Aerobic respiration 210 11.3 Glycolysis 210 11.4 Tricarboxylic acid cycle 217 11.5 Electron transport and oxidative

phosphorylation 221 11.6 The yield of ATP 223 11.7 Catabolism of unusual carbohydrates 224 11.8 Catabolism of organic acids 225 11.9 Catabolism of organic substrates other

than carbohydrates 225 11.10 Further reading 225

CHAPTER 12

Anaerobic respiration 227 12.1 Definition 227 12.2 Diversity of microorganisms 227 12.3 Electron transport chain 228 12.4 Electron acceptors and energy

conservation 229 12.5 Dissimilatory and assimilatory

reductions 229 12.6 Diversity of respiratory pathways 231 12.7 Further reading 245

CHAPTER 13

Fermentation 246

13.1 Introduction 246

13.2 Definition 246 13.3 Physiological significance of

fermentations 247 13.4 Types of fermentations 248 13.5 Pyruvate, a key compound in

fermentations 249 13.6 Fermentation vs oxygen 251 13.7 Alcohol fermentation 252 13.8 Lactic acid fermentation 255 13.9 Propionate fermentation 259 13.10 Mixed acid fermentation 263 13.11 Butanediol fermentation 265 13.12 Butyrate-butanol fermentation 267 13.13 Ethanol-acetate fermentation 269 13.14 Fermentation of amino acids 271 13.15 Fermentation balances 272 13.16 Ruminococcus albus: A model for

interspecies hydrogen transfer syntrophy 274

13.17 Anaerobic food chain 275 13.18 Further reading 276

CHAPTER 14

Biological nitrogen fixation 278

14.1 Introduction 278 14.2 Nitrogen fixing microorganisms 279 14.3 Outlines of nitrogen fixation 280 14.4 Requirements of nitrogen fixation 282 14.5 Mechanism of nitrogen fixation 287 14.6 Further reading 297

CHAPTER 15

Secondary metabolism 298

15.1 Introduction 298 15.2 The concept of primary and secondary

metabolites 298 15.3 Characteristics of secondary

metabolites 299 15.4 The significance of secondary

metabolites 301 15.5 Biosynthetic pathways of secondary

metabolites 301

Contents xii

15.6 Some important secondary metabolites 306 15.7 Further reading 311

CHAPTER 16

Sporulation 313

16.1 Introduction 313 16.2 Endospore structure 314

16.3 Endospore formation 315 16.4 Endospore germination 319 16.5 Further reading 320 Glossary 321

Index 332